Uranium and plutonium are typical actinides tightly associated with nuclear fuel cycle. In this work we rationally design and fabricate a phosphonic group-decorated covalent organic framework, TzDa-Phos, for highly selective removal of uranium [U(VI)] and plutonium [Pu(IV)]. The saturation adsorption capacity for U(VI) can reach 394 mg/g at pH 4.0, and even maintains 40 mg/g in 1–4 M HNO3 solutions. The distribution coefficient of Pu(IV) with TzDa-Phos is recorded up to 9.7 × 103 mL/g at 3 M HNO3. The excellent adsorption performance of TzDa-Phos for U(VI) and Pu(IV) is reasonably attributed to phosphonic groups decorated in TzDa. Specifically, the strong complexation of PO with uranium nitrate species (e.g., UO2(NO3)+, UO2(NO3)20) is indicated at high acidities, in contrary to the coordination of P-O− with uranium at pH 4.0 as evidenced by FT-IR, XPS and EXAFS analyses. This work provides a promising adsorbent to recover uranium and plutonium from various wastewaters via a solid-phase extraction approach.